/*    This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
 *    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
 *    Author(s):       Clément Maria, Marc Glisse
 *
 *    Copyright (C) 2014 Inria
 *
 *    Modification(s):
 *      - YYYY/MM Author: Description of the modification
 */

#include <gudhi/Simplex_tree.h>
#include <gudhi/Persistent_cohomology.h>
#include <gudhi/Rips_complex.h>
#include <gudhi/Hasse_complex.h>
#include <gudhi/Points_off_io.h>
#include <gudhi/distance_functions.h>

#include <boost/program_options.hpp>

#include <string>
#include <vector>

////////////////////////////////////////////////////////////////
//                                                            //
//  WARNING: persistence computation itself is not parallel,  //
//  and this uses more memory than rips_persistence.          //
//                                                            //
////////////////////////////////////////////////////////////////

// Types definition
using Simplex_tree = Gudhi::Simplex_tree<>;
using Filtration_value = Simplex_tree::Filtration_value;
using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
using Point = std::vector<double>;
using Points_off_reader = Gudhi::Points_off_reader<Point>;

void program_options(int argc, char * argv[]
                     , std::string & off_file_points
                     , std::string & filediag
                     , Filtration_value & threshold
                     , int & dim_max
                     , int & p
                     , Filtration_value & min_persistence);

int main(int argc, char * argv[]) {
  std::string off_file_points;
  std::string filediag;
  Filtration_value threshold;
  int dim_max;
  int p;
  Filtration_value min_persistence;

  program_options(argc, argv, off_file_points, filediag, threshold, dim_max, p, min_persistence);

  Points_off_reader off_reader(off_file_points);
  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance());

  // Construct the Rips complex in a Simplex Tree
  Simplex_tree& st = *new Simplex_tree;
  rips_complex_from_file.create_complex(st, dim_max);

  std::clog << "The complex contains " << st.num_simplices() << " simplices \n";
  std::clog << "   and has dimension " << st.dimension() << " \n";

  // Sort the simplices in the order of the filtration
  st.initialize_filtration();
  int count = 0;
  for (auto sh : st.filtration_simplex_range())
    st.assign_key(sh, count++);

  // Convert to a more convenient representation.
  Gudhi::Hasse_complex<> hcpx(st);

  // Free some space.
  delete &st;

  // Compute the persistence diagram of the complex
  Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::Hasse_complex<>, Field_Zp > pcoh(hcpx);
  // initializes the coefficient field for homology
  pcoh.init_coefficients(p);

  pcoh.compute_persistent_cohomology(min_persistence);

  // Output the diagram in filediag
  if (filediag.empty()) {
    pcoh.output_diagram();
  } else {
    std::ofstream out(filediag);
    pcoh.output_diagram(out);
    out.close();
  }
}

void program_options(int argc, char * argv[]
                     , std::string & off_file_points
                     , std::string & filediag
                     , Filtration_value & threshold
                     , int & dim_max
                     , int & p
                     , Filtration_value & min_persistence) {
  namespace po = boost::program_options;
  po::options_description hidden("Hidden options");
  hidden.add_options()
      ("input-file", po::value<std::string>(&off_file_points),
       "Name of file containing a point set. Format is one point per line:   X1 ... Xd ");

  po::options_description visible("Allowed options", 100);
  visible.add_options()
      ("help,h", "produce help message")
      ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
       "Name of file in which the persistence diagram is written. Default print in std::clog")
      ("max-edge-length,r", po::value<Filtration_value>(&threshold)->default_value(0),
       "Maximal length of an edge for the Rips complex construction.")
      ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
       "Maximal dimension of the Rips complex we want to compute.")
      ("field-charac,p", po::value<int>(&p)->default_value(11),
       "Characteristic p of the coefficient field Z/pZ for computing homology.")
      ("min-persistence,m", po::value<Filtration_value>(&min_persistence),
       "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals");

  po::positional_options_description pos;
  pos.add("input-file", 1);

  po::options_description all;
  all.add(visible).add(hidden);

  po::variables_map vm;
  po::store(po::command_line_parser(argc, argv).
            options(all).positional(pos).run(), vm);
  po::notify(vm);

  if (vm.count("help") || !vm.count("input-file")) {
    std::clog << std::endl;
    std::clog << "Compute the persistent homology with coefficient field Z/pZ \n";
    std::clog << "of a Rips complex defined on a set of input points.\n \n";
    std::clog << "The output diagram contains one bar per line, written with the convention: \n";
    std::clog << "   p   dim b d \n";
    std::clog << "where dim is the dimension of the homological feature,\n";
    std::clog << "b and d are respectively the birth and death of the feature and \n";
    std::clog << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;

    std::clog << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
    std::clog << visible << std::endl;
    exit(-1);
  }
}